6EFN | pdb_00006efn

Structure of a RiPP maturase, SkfB

• PDB DOI: https://doi.org/10.2210/pdb6EFN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-16 Released: 2018-10-24 
• Deposition Author(s): Grell, T.A.J., Drennan, C.L.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Structure of a RiPP maturase, SkfB

Grell, T.A.J., Kincannon, W.M., Bruender, N.A., Blaesi, E.J., Krebs, C., Bandarian, V., Drennan, C.L.

(2018) J Biological Chem 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.95 kDa 
• Atom Count: 3,656 
• Modeled Residue Count: 383 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sporulation killing factor maturation protein SkfB	A	412	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: skfB, ybcP, ybcQ, BSU01920 EC: 1.21.98
UniProt
Find proteins for O31423 (Bacillus subtilis (strain 168)) Explore O31423  Go to UniProtKB:  O31423

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)	D [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.462	α = 90
b = 83.11	β = 94.38
c = 61.299	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Grell, T.A.J., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1122374

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations